Pluripotent cells from the mammalian late epiblast layer

ABSTRACT

The invention relates to the isolation and propagation of pluripotent cells isolated from the mammalian late epiblast layer, termed Epiblast Stem Cells (EpiSCs). These cells are useful in a range of applications, including the generation of transgenic animal species.

This application is a divisional application of U.S. National Stageapplication Ser. No. 12/312,395, filed May 9, 2009 and claims priorityunder 35 USC §119 to International Application No. PCT/GB2007/004302,filed Nov. 9, 2007, which claims priority to Great Britain ApplicationNo. 0622395.2, filed Nov. 9, 2006, the contents of which areincorporated herein by reference in their entirety.

This invention relates to the production and culture of pluripotentmammalian cells.

While the first mouse embryonic stem cell (mESC) lines were derived 25years ago (Evans, 1981, Martin, 1981) using feeder layer-basedblastocyst cultures, subsequent efforts to extend the approach to othermammals, including both laboratory and domestic species, have beenrelatively unsuccessful. The most notable exceptions were the derivationof primate ES cell lines by Thomson and colleagues (Thomson, 1995,Thomson, 1996) followed shortly by their derivation of human ES cells(hESCs) (Thomson, 1998). Despite the similarity of hESC derivationmethodology, undifferentiated proliferation and developmentalpluripotency to the properties of mouse ESCs, early studies revealedbasic differences between them. In addition to having distinct cellsurface markers, hESCs were unresponsive to Leukaemia Inhibitory Factor(LIF), which is able to maintain mouse ESC pluripotency inserum-containing medium (Thomson, 1998, Daheron, 2004) and BMP4, whichcooperates with LIF to maintain mESC pluripotency in serum-freeconditions (Ying, 2003), induces rapid differentiation of hESC intoextraembryonic cell types (Xu, 2002). Finally, it has recently beenestablished (Vallier, 2004, Vallier, 2005, Beattie, 2005, James, 2005)that hESCs rely instead on Activin/Nodal and FGF (Xu, 2005, Levenstein,2006) signalling pathways to maintain their pluripotent status.

The present inventors have isolated and propagated a previouslyunreported type of pluripotent cell, termed ‘Epiblast Stem Cells’(EpiSCs). These cells are useful in a range of applications, includingthe generation of transgenic animal species.

One aspect of the invention provides a method of producing pluripotentcells from a mammal comprising:

culturing one or more mammalian late epiblast cells in a chemicallydefined medium in the presence of an activin agonist.

A pluripotent mammalian cell is an unspecialized cell that is capable ofreplicating or self renewing itself and developing into specializedcells of all three primary germ layers i.e. ectoderm, mesoderm and 5endoderm but are not able to develop into all embryonic andextra-embryonic tissues, including trophectoderm (i.e. not totipotent).Pluripotent cells arise from the division of totipotent cells.

Mammalian late epiblast cells are cells of the embryo after itspluripotent cells have undergone cavitation to form a simple epitheliallayer (the late epiblast layer) after implantation i.e. pre- or earlygastrulation (e.g. mouse embryo 5.0-6.5 d.p.c). Suitable cells may beobtained by isolating the late epiblast layer of a mammalian embryo and,optionally, isolating one or more cells from said layer.

Preferably, the late epiblast cells are separated and/or isolated fromextraembryonic cells. This may be performed using routine techniques.For example, the late epiblast layer of an embryo may be separated fromextraembryonic tissues by microdissection. Microdissection may beperformed in a suitable buffer (e.g. Cell Dissociation Buffer;Invitrogen) at 4° C. for 15-20 mins or Collagenase (Type IV, Gibco, 1mg/ml) medium at room temperature for 5-15 mins to promote dissociationof the layers.

The mammal may be a human or a non-human mammal, for example a rodent(e.g. a guinea pig, a hamster, a rat, a mouse), a marsupial (e.g., anopossum), a canine (e.g. a dog), a feline (e.g. a cat), a porcine (e.g.a pig), a bovine (e.g. cattle), an ovine (e.g. sheep), a caprine (e.g.goat), an equine (e.g. a horse), a non-human primate, such as a simian(e.g. a monkey or ape), a monkey (e.g. marmoset, baboon) or an ape (e.g.orang-utan, gorilla, chimpanzee, gibbon).

A chemically defined medium (CDM) is a nutritive solution for 35culturing cells which contains only specified components, preferablycomponents of known chemical structure.

A suitable chemically defined medium may comprise a basal culturemedium, such as IMDM and/or F12 supplemented with insulin, for exampleat 0.5 ug/ml to 70 ug/ml, transferin, for example at a concentration of5 1.51-ig/ml to 150 ug/ml, 1-thiolglycerol, for example at aconcentration of 45 uM to 4.5 mM and BSA (or PVA), for example at aconcentration of 0.5 mg/ml to 50 mg/ml.

Suitable CDM include the CDM of Johansson and Wiles (1995) consistingof: standard IMDM/F12 base (Life Technologies Inc., Gaithersburg, Md.,USA) 7 ng/ml insulin, 15 ug/ml transferrin, 2.5 g/ml BSA (or 0.1% PVA),1% chemically defined lipid concentrate (Invitrogen), and 350 uM1-thiolglycerol. Other suitable CDM may comprise 50% IMDM plus 50% F12NUT-MIX, supplemented with 7 ug/ml of insulin, 15 ug/ml of transferrin,450 uM of monothioglycerol and 5 mg/ml bovine serum albumin fraction V.

Media and ingredients thereof may be obtained from commercial sources(e.g. Gibco, Roche, Sigma, Europabioproducts). BSA may be replaced inCDM by Polyvinyl alcohol (PVA), human serum albumin, Plasmanate™ (humanalbumin, alpha-globulin and beta globulin: Talecris Biotherapeutics N.C.USA) or Buminate™ (human albumin: Baxter Healthcare), all of which areavailable from commercial sources.

Other suitable CDM which may be used in accordance with the presentmethods are known in the art (e.g. N12 medium).

An activin agonist is a compound which activates the Activin/Nodalsignalling pathway, for example by binding to TGFbeta or activinreceptors. Examples of activin agonists include activin A, activin B,activin AB, TGFbetal, Growth and Differentiation Factor (GDF)-3, andNodal.

Known activin receptors include heterodimers between type I activinreceptors (ACVR1 GeneID: 90 NCBI reference NP_(—)001096.1 GI: 4501895)and type II activin receptors (ACVR1B GeneID: 91 NCBI referenceNP_(—)004293.1 GI: 4757720 or ACVR1C GeneID: 130399 NCBI referenceNP_(—)660302.1 GI: 21687098).

Known TGFbeta receptors include heterodimers between type I TGFbetareceptors (TGFBR1 GeneID: 7046 NCBI reference NP_(—)004603.1 GI:4759226) and type II TGFbeta receptors (TGFBR2 GeneID: 7048 NCBIreference NP_(—)001020018.1 GI: 67782326).

Activin A and activin B are dimeric polypeptides which exert a range ofcellular effects via stimulation of the Activin/Nodal pathway, which ismediated by Smad 2 and Smad 3. Activin A is a homodimer of human activinA (NCBI GeneID: 3624 nucleic acid reference sequence NM_(—)002192.2 GI:62953137, amino acid reference sequence NP_(—)002183.1 GI: 4504699) oractivin A from another mammalian species. Activin B is a homodimer ofhuman activin B (NCBI GeneID: 3625, nucleic acid reference sequenceNM_(—)002193.1 GI: 9257224 amino acid reference sequence NP 002184.1 GI:9257225) or Activin B from another mammalian species. Activin AB is aheterdimer comprising activin A and activin B subunits. Activin A, B andAB are available commercially (e.g. SBH Sciences, Mass. USA).

Transforming growth factor, beta 1 (TGFbetal) may be human TGFbetal(GeneID: 7040 nucleic acid reference sequence NM_(—)000660.3 GI:63025221, amino acid reference sequence NP_(—)000651.3 GI: 63025222) orTGFbetal from 25 another mammalian species. TGFbetal is availablecommercially (e.g. Sigma-Aldrich).

Growth Differentiation Factor (GDF)-3 may be human GDF-3 (GeneID: 9573;nucleic acid reference sequence NM_(—)020634.1 GI: 10190669; amino acidreference sequence NP_(—)065685.1 GI:10190670) or GDF-3 from anothermammalian species. GDF-3 is described, for example, in Chen et alDevelopment (2006) 133 319-329.

Nodal may be human Nodal (GeneID: 4838 nucleic acid reference sequence35 NM_(—)018055.3 GI: 38176152, amino acid reference sequenceNP_(—)060525.2 GI: 29568107) or Nodal from another mammalian species.Nodal is available commercially (e.g. Sigma-Aldrich).

Conveniently, the concentration of the activin agonist in the CDM may befrom 1 to 100 ng/ml, preferably about 10 ng/ml.

The CDM may further comprise fibroblast growth factor 2 (FGF2) (e.g.human FGF2 NCBI GeneID: 2247, nucleic acid sequence NM_(—)002006.3 GI:41352694, amino acid sequence NP_(—)001997.4 GI: 41352695) Human 10recombinant FGF2 is available from commercial suppliers (e.g. R&D,Minneapolis, Minn., USA).

Conveniently, the concentration of FGF2 in the medium may be from 1 to100 ng/ml, preferably about 12 ng/ml.

Preferably, the cells are cultured in the absence of BMP4.

Mammalian late epiblast cells may be cultured using routine mammaliancell culture techniques, for example on fibronectin or fetal bovineserum (FBS) coated plates in the above medium. Methods and techniquesfor the culture of mammalian cells are well-known in the art (see, forexample. Basic Cell Culture Protocols, C. Helgason, Humana Press Inc.U.S. (15 Oct. 2004) ISBN: 1588295451; Human Cell Culture Protocols(Methods in Molecular Medicine S.) Humana Press Inc., U.S. (9 Dec. 2004)ISBN: 1588292223; Culture of Animal Cells: A Manual of Basic Technique,R. Freshney, John Wiley & Sons Inc (2 Aug. 2005) ISBN: 0471453293, Ho WY et al J Immunol Methods. (2006) 310:40-52, Handbook of Stem Cells (ed.R. Lanza) ISBN: 0124366430). In preferred embodiments, EpiSCs may bepassaged using collagenase and mechanical dissociation, in accordancewith standard techniques.

Standard mammalian cell culture conditions may be employed, for example37° C., 21% Oxygen, 5% Carbon Dioxide. Media is preferably changed everyone day and cells allowed to settle by gravity.

EpiSCs may be further maintained and propagated in the medium.

EpiSCs produced as described above may be allowed to differentiate, forexample into a lineage of one of the three germ layers; endoderm,mesoderm and neuroectoderm. For terminal differentiation, EpiSCs may becultured in the absence of growth factors, for example in DMEM/2% B27(Invitrogen) or CDM or other suitable media, which may also includecombinations of established factors for the production of particularcell lineages.

For example, EpiSCs may be cultured in a chemically defined medium (CDM)supplemented with one or more differentiation factors and allowed todifferentiate into partially differentiated progenitor cells or fullydifferentiated cells.

Differentiation factors include growth factors which modulate one ormore of the Activin/Nodal, FGF, Wnt or BMP signalling pathways. Examplesof differentiation factors include FGF2, BMP4, retinoic acid, TGFbeta,GDF3, LIF, IL and activin.

To produce progenitor cells of an ectoderm lineage, for example aneuroectoderm lineage, EpiSCs may be cultured in a chemically definedmedium (CDM) supplemented with FGF2 and an Activin antagonist, such asSB431542 (Sigma, Tocris) or a soluble protein factor such as Lefty,Cerberus or follistatin, and allowed to differentiate into partiallydifferentiated progenitor cells or fully differentiated cells. Fullydifferentiated cells may include neural cells such as neurons, and glialcells, such as astrocytes and oligodendrocytes.

To produce progenitor cells of a mesendoderm lineage (i.e. eithermesoderm or endoderm lineages), EpiSCs may be cultured in a chemicallydefined medium (CDM) supplemented with Activin, FGF2 and BMP4, andallowed to differentiate into partially differentiated progenitor cellsor fully differentiated cells.

Differentiated cells produced from EpiSCs may be useful in a range ofapplications, including drug screening, in vitro modelling, andtransplantation.

Another aspect of the invention provides a pluripotent mammalian cellproduced or obtainable by a method described herein.

Pluripotent mammalian cells (EpiSCs) produced by the present methodshave a number of characteristic features. For example, EpiSCs expressspecific markers of the epiblast layer of the post-implantation embryo,such as FGF5 and Nodal, and do not express specific markers of the innercell mass (i.e. blastocyte cells), such as GBX2 or Rexl and do notexpress markers of germ cells such as Blimpi, Stella, and alkalinephosphatase. EpiSCs also express the pluripotency markers Oct-4, Nanogand Sox2 are able differentiate into endoderm, mesoderm or neuroectodermcells.

Unlike blastocyst-derived pluripotent cells, EpiSCs are unresponsive toLeukaemia Inhibitory Factor (LIF) and differentiate into extra-embryoniclineages in response to BMP4.

EpiSCs produced by the present methods may be substantially free fromother cell types. In some embodiments, EpiSCs may be separated fromother cell types using any technique known to those skilled in the art,including those based on the recognition of extracellular epitopes byantibodies and magnetic beads or fluorescence activated cell sorting(FACS) including the use of antibodies against extracellular regions ofpluripotency markers such as SSEA-1.

As described above, pluripotent mammalian cells (EpiSCs) may be derivedfrom a human or a non-human mammal, such as a mouse.

EpiSCs or ancestor cells thereof may be genetically manipulated, forexample to reduce or silence expression of one or more genes or to 35express one or more heterologous polypeptide.

EpiSCs may be genetically modified during in vitro growth as describedherein, for example by the introduction of a heterologous nucleic acid,such as a nucleic acid construct or vector, into the cells in theculture medium. This may be useful in expressing a marker or reportergene or a therapeutic or other sequence of interest. For example, aheterologous protein may be over-expressed by stable transfection,expression of an endogenous gene may be knocked down or suppressed usingSiRNA or knocked out using homologous recombination. Alternatively areporter gene may be expressed using stable transfection or knock in byhomologous recombination, or mutations may be generated usingethylnitrosourea (ENU) for mutant screening.

When introducing or incorporating a heterologous nucleic acid into anEpiSC, certain considerations must be taken into account, well known tothose skilled in the art. The nucleic acid to be inserted should beassembled within a construct or vector which contains effectiveregulatory elements which will drive transcription in the target cell.Suitable techniques for transporting the constructor vector into thecell are well known in the art and include calcium phosphatetransfection, DEAE-Dextran, electroporation, liposome-mediatedtransfection and transduction using retrovirus or other virus, e.g.vaccinia or lentivirus. For example, solid-phase transduction may beperformed without selection by culture on retronectin-coated, retroviralvector-preloaded tissue culture plates.

Many known techniques and protocols for manipulation and transformationof nucleic acid, for example in preparation of nucleic acid constructs,introduction of DNA into cells and gene expression, and analysis ofproteins, are described in detail in Protocols in Molecular Biology,Second Edition, Ausubel et al. eds. John Wiley & Sons, 1992 andMolecular Cloning: a Laboratory Manual: 3rd edition, Sambrook & Russell,2001, Cold Spring Harbor Laboratory Press.

EpiSCs as described herein may be useful in the production of non-humanmammals.

In some embodiments, an EpiSC may be injected into a blastocyst of saidnon-human mammal to produce a chaemeric embryo and the chaemeric embryois then allowed to develop to term. The chaemeric embryo may be allowedto develop to term in its native mother or may be implanted into asurrogate to develop to term.

In other embodiments, EpiSCs may be aggregated with the embryo of anon-human mammal at the morula stage to produce a chaemeric embryo whichis then allowed to develop to term. This may be achieved using standardtechniques in the art. For example, EpiSCs may be aggregated. The zonapellucida may be removed from the embryo of the non-human mammal and anaggregate of EpiSCs added to the embryo. The embryo may then be culturedand allowed to develop into a chaemeric blastocyte. The chaemericblastocyte may be allowed to develop to term in its native mother or maybe implanted into a surrogate to develop to term.

In other embodiments, an EpiSC nucleus may be isolated and introducedinto an unfertilised recipient mammalian egg cell, preferably anon-human mammalian egg cell. This may be useful, for example, incloning non-human mammals or producing multipotent or pluripotent cells,for example embryonic stem or progenitor cells.

Suitable mammalian egg cells are arrested in the second metaphase ofmeiotic maturation.

Mammalian egg cells may be obtained from any suitable donor. Suitableegg cells may be collected from the reproductive tracts of ovulatinganimals using conventional surgical or non-surgical methods. Suitableegg cells may be matured in vitro using standard techniques fromimmature cells collected from the ovaries of a donor animal.

The egg cell nucleus may be removed or destroyed prior to introductionof the EpiSC nucleus (i.e. the egg cell may be enucleated), for example,by manually removing the nucleus with a micro-pipette, or by cautery.Alternatively, the egg cell nucleus may be removed after theintroduction of the EpiSC cell nucleus.

The recipient egg cell may be from a different mammalian source to theEpiSC nucleus or, more preferably, from the same mammalian source.

Recipient egg cells containing an EpiSC nucleus may be cultured togenerate populations of cells and cell lines, in particular pluripotentor multipotent cells and cell lines. Tissues, embryos and/or non-humananimals may be generated from a population of said cells usingtechniques well known in the art (Wakayama et al (2001) Science 292;740-743).

Following introduction of the EpiSC nucleus, embryonic development mayinitially be in vitro and subsequently in a surrogate. Thus, the eggcell may be initially cultured in vitro to produce a blastocyst orembryo and then the embryo may be transferred to a surrogate forsubsequent development into a non-human mammal. Alternatively, embryonicdevelopment may be in vivo and the cell may be implanted into asurrogate directly after the EpiSC nucleus is introduced. The generationof non-human embryos and mammals from implanted nuclei is now wellestablished in the art (Campbell K H, et al. (1996) Nature. 380:64-66,Wilmut I et al. (1997) Nature (London) 385:810-813, ‘Principles ofCloning’ Ed: Jose Cibelli et al ISBN 0-12-174597-X).

Transgenic non-human animals produced as described herein may be usefulas models for disease conditions or as sources of tissue forxenotransplantation.

Another aspect of the invention provides a method of producing orexpanding a population of pluripotent mammalian cells comprising:

culturing one or more pluripotent mammalian cells in a chemicallydefined medium in the presence of an activin agonist and, optionallyFGF2,

thereby producing or expanding the population of said cells.

Populations of pluripotent mammalian cells which may be produced orexpanded in this way include human embryonic stem cell (hESCs) andEpiblast stem cell (EpiSCs) populations.

The population of pluripotent mammalian cells may predominately expressOct-4, Sox2 and Nanog, for example, at least 70%, at least 80% or atleast 90% of the cells in said population may express one or more, twoor more, three or more or all four of these markers. Human pluripotentcells may also express Tra-1-60, and SSEA-3 and mouse pluripotent cellsmay also express SSEA-1.

The cells may be cultured using conventional cell culture techniques, asdescribed above. Chemically defined media are described in more detailabove and include Johannsen and Wiles CDM containing insulin,transferrin, defined lipids and Bovine or Human Serum Albumin (BSA).

Another aspect of the invention provides the use of a chemically definedmedium supplemented with an activin agonist and, optionally, FGF2, inthe culture of pluripotent mammalian cells, in particular pluripotentnon-human mammalian cells.

Suitable media are described above.

Various further aspects and embodiments of the present invention will beapparent to those skilled in the art in view of the present disclosure.All documents mentioned in this specification are incorporated herein byreference in their entirety.

The invention encompasses each and every combination and sub-combinationof the features that are described above.

Certain aspects and embodiments of the invention will now be illustratedby way of example and with reference to the figures described above andtables described below.

FIG. 1 shows that hESCs grown in CDM supplemented with Activin (10ng/ml) and FGF2 (12 ng/ml) express homogenously pluripotency markersTra-1-60 and SSEA-3. hESCs were grown for 85 passages (˜250 days) inadherent conditions and then the fraction of pluripotent cells wasestablished using FACS to detect expression of SSEA-3 (right panel) andTra-1-60 (left panel).

FIG. 2 shows a comparison of expression profile of ICM from embryos atthe blastocyst stage, late epiblast from embryos at post implantationstages, mESCs and mEpiSCs, using MDS plot.

Table 1 shows the efficiency of derivation of EpiSCs from rat and mouseembryos.

EXPERIMENTS

Material and Methods

EpiSC and hESCs culture in feeder free and serum free conditions.

For feeder and Serum free culture, hESCs (H9 and HI (WiCell, Madison,Wis.), hSF-6 (UCSF, San Francisco, Calif.)) and EpiSCs were grown inchemically defined medium (CDM), supplemented with Activin (10 ng/ml,RandD systems) and FGF2 (12 ng/ml, RandD systems). The composition ofCDM was 50% IMDM (Gibco) plus 50% F12 NUT-MIX (Gibco), supplemented with7 ug/ml of insulin (Roche), 15 ug/ml of transferrin (Roche), 450 uM ofmonothioglycerol (Sigma) and 5 mg/ml bovine serum albumin fraction V(Europabioproducts). Every 4 days, cells were harvested using 5 mg/mlcollagenase IV (Gibco) or Accutase (BioWest) and then plated into plates(Costar) pre-coated with 15 ug/ml of human Fibronectin (Chemicon) for 20minutes at 37 C and then washed twice in PBS.

RNA Extraction and Real Time PCR

Total RNAs were extracted from mouse ESCs or EpiSCs or theirdifferentiated derivatives using the RNeasy Mini Kit (Qiagen). Eachsample was treated with RNAse-Free DNAse (Qiagen) in order to avoid DNAcontamination. For each sample 0.6 ug of total RNA was reversetranscribed using Superscript II Reverse Transcriptase (Invitrogen).

Real time PCR reactions mixture were prepared as described (Promega)then were denatured at 94° C. for 5 minutes and cycled at 94° C. for 30seconds, 60° C. for 30 seconds, and 72° C. for 30 seconds followed byfinal extension at 72° C. for 10 minutes after completion of 35 cycles.Primer sequences were designed using the primer bank web software(http://pga.mgh.harvard.edu/primerbank/).

Immunofluorescence

hESCs, mouse ESCs or EpiSCS were fixed for 20 minutes at 4° C. in 4%paraformaldehyde (PFA) and then washed three times in PBS. Cells wereincubated for 20 minutes at room temperature in PBS containing 10% goatserum (Serotec) and subsequently incubated over night at 4° C. withprimary antibody diluted in 1% goat serum in PBS as follows: SSEA-3(1:100, Santa Cruz), SSAE-1 (1:25, gift from PW Andrews), Tra-1-60(1:100, Santa CruZ), Oct-4 (1:100, SantaCruz), Sox2 (1:100, AbeamabI5830), Nanog (1:100, Abeam), Blirnpl (Abeam). Cells were then washedthree times in PBS and incubated withfluorescein-Isothiocyanate-conjugated anti-mouse IgG or IgM (Sigma 1:200in 1% goat serum in PBS) or rat IgM (Jackson laboratory 1:300 in goatserum in PBS) or rabbit IgG (Jackson laboratory 1:200 in donkey serum inPBS) for two hours at room temperature. Unbound secondary antibody wasremoved by 3 washes in PBS. Hoechst 33258 was added to the first wash(Sigma 1:10000).

Microarray Methods

RNA extraction and cDNA labelling: Total RNAs were extracted from mouseESCs (B6xCBA)FI passage 15, EpiSCs (B6xCBA)FI passage 15, pure epiblastlayer dissected from embryo at 5.5 d.p.c. or mouse blastocyst (B6xCBA)FIwere extracted amplified and labelled as described by Tietjen et al.

Microarray data processing: Sample RNA was hybridized to Affymetrix(mg-u74Av2/hg-ul33+2) GeneChips®. All sample arrays were backgroundcorrected, normalized and summarized using default parameters of the RMAmodel2. Array processing was performed using the affy package of theBioconductor (http://www.bioconductor.org) suite of software for the Rstatistical programming language (http://www.r-project.org).

The resulting data sets contained processed gene expression values for54675 probe-sets (Affymetrix hg-u133+2 chip)/12488 probe-sets(Affymetrix mg-u74Av2 chip).

Analysis of Differential Regulation: The moderated t-statistic of Smythet al, implemented in the Limma package of Bioconductor, was employed toassess the significance of differential gene (probe-set) expressionbetween sample groups. In order to reduce errors associated withmultiple hypothesis testing on such a scale, the significance 10p-values obtained were converted to corrected q-values using the FDRmethod of Storey et al. Probe-sets with associated q<0.01 (FDR 1%) weredeemed to exhibit significant differential expression between samplegroups.

Data Visualisation: Heat maps of gene expression were created byimporting relevant subsets of RMA processed microarray gene expressiondata into the dChip vl.3 microarray analysis package(http://www.biostat.harvard.edu/complab/dchip/). The dissimilaritybetween two microarray expression profiles of equal length was assessedwith a bounded distance measure of [1.0—Pearson correlation] anddisplayed using multidimensional scaling (MDS) plots.

Teratomas

H9 cells or EpisSCs (B6xCBA)FI were harvested mechanically immediatelyprior to implantation and approximately 10⁵ cells were inoculatedbeneath the testicular capsule 7 of C.B.-17/GbmsTac-scid-bgDF N7 miceage 6 weeks (M&B, Denmark). The mice (5 per group) were sacrificed after60 days and then the injected testes were cut into equal pieces using arazor blade. The material was fixed overnight in 4% neutral bufferedformaldehyde, and dehydrated through a graded series of alcohols toxylene. The tissue was embedded in paraffin and serially sectioned at 5um followed by characterization. Normal non-injected testes served ascontrols.

Results

Chemically defined culture conditions for growing hESCs in the absenceof serum and feeders were developed using the chemically defined medium(CDM) of Johannsen and Wiles {Johansson, 1995 ttl32} containing insulin,transferrin, defined lipids, Bovine Serum Albumin (BSA) to which weadded Activin 10 ng/ml, FGF2 12 ng/ml. H9, HI and hSF-6 hESCs grown onhuman fibronectin coated plates in CDM+Activin+FGF (CDM/AF) overprolonged periods were assessed for expression of pluripotency markersby immunofluorescence and found to maintain the expression of thepluripotency markers Oct-4, Sox2, Tra-1-60, and SSEA-3. FACs analysesshowed that the fraction of hESCs expressing the cell surface antigensTra-1-60 and SSEA-3 were maintained at 95% and 87% after 85 passages inthese culture conditions (FIG. 1).

Karyotype analyses showed that hESCs remained genetically stable andmaintained a normal karyotype under these conditions. In addition, DNAmethylation and monoallelic expression of imprinted genes remainednormal, suggesting that they did not undergo any epigenetic alterations.Finally, teratomas from H9 cells were grown in CDM/AF. Approximately5×10⁶ H9 hESCs grown for 40 passages in CDM/AF were injected in thetestis capsule of SCID-beige mouse and the resulting tumors wereharvested 3 months after injection and assessed. hESCs thus culturedwere found to be capable of forming teratomas when transplanted inimmunodeficient mice confirming the pluripotent status of the cells.

Together, these results definitively demonstrate that hESCs can be grownin chemically defined condition (CDM/AF on Fibronectin coated plates)for long periods without losing their genetic or epigenetic 30 integrityor their pluripotency.

Similar culture conditions were tested for derivation of pluripotentcells from pre- and post-implantation rodent embryos. Entire mouseblastocysts grown in CDM/AF never gave rise to pluripotent cell lines(Table 1) showing that these culture conditions are not suitable forgrowing blastocyst derived embryonic stem cells. For derivation at postimplantation stages, the late epiblast layer of embryos at pre- or earlygastrulation stages (5.5 dpc or 6.5 dpc) was separated fromextraembryonic tissues by microdissection using Cell Dissociation Buffer(Invitrogen) at 4° C. for 15-20 min. to promote dissociation of thelayers. The resulting pure epiblast cell layers were then cultivated onfibronectin or fetal bovine serum (FBS) coated plates in CDMsupplemented with 20 ng/ml of Activin A and 12 ng/ml of FGF2. After 24hours, the epiblast layers formed colonies of compact cells having ahigh nucleo-cytoplasmic ratio, a characteristic morphological trait ofpluripotent embryonic stem cells. Cells on the edge of the colonystarted to differentiate the following day, thereby producing a broadring of stromal cells surrounding smaller aggregates of compact cells.These heterogeneous populations proceeded to form larger colonies ofcells 4-5 days later. The latter colonies were picked, dissociated intosmaller clumps using collagenase IV (Invitrogen) and then transferred tonew dishes. Resulting colonies were passaged again 5 days later usingcollagenase and mechanical dissociation. Immunostaining analyses carriedout after 20 passages showed that the colonies of compact cellsexpressed the pluripotency markers Oct-4, Nanog and SSEA-1. These cellswere designated Epiblast Stem Cells (EpiSCs) on the basis of theirorigin from pure epiblast cell layers.

The expression of pluripotency markers Oct-4, Nanog and SSEA-1 wasanalysed in mouse ESCs of 129 strain grown on feeders in mediumcontaining FBS and LIF and in mouse EpiSCs of the NOD genetic backgroundand in rat EpiSCs of the Wistar strain grown for prolonged periods inCDM supplemented with Activin (and FGF2 for mEpiSCs) usingimmunoflurescence. Once established, EpiSC cells could be maintained formore than 40 passages while maintaining their expression of Oct-4,Nanog, Sox2 and SSEA-1. The success rate of derivation was 83% for(B6xCBA)FI and 90% for the NOD genetic background (Table 1), the latterbeing particularly challenging for the derivation of mESCs (Brook,2003). Interestingly, EpiSCs grew as flat, compact colonies similarly tohESCs cultivated under the same culture conditions, and were distinctfrom mESCs, which form rounded, rather than flattened, colonies. Inaddition, passaging of single cell EpiSCs using trypsin or other singlecell dissociation methods induced cell death or differentiation astypical for hESCs (and contrary to mouse ES cells), showing a lowefficiency of clonal growth.

Dissected mouse epiblasts were grown in CDM supplemented with BMP4 (50ng/ml) and LIF, two growth factors required to maintain the pluripotentstatus of mouse ESCs. After 24 hours, epiblast colonies grown in theseconditions contain large number of cells with pluripotent-likemorphology (high nucleocytoplasmic ratio, etc. However, all these cellshad differentiated by the fourth day and they had formed complex tissuesby the following day. We were not able to derive any EpiSC lines in thepresence of LIF or/and BMP4.

Rat EpiSCs were grown in CDM supplemented in the presence of Activin (10ng/ml), SB431542 (10 uM), BMP4 10 ng/ml+SB431542 (10 uM) or Activin (10ng/ml)+Noggin (100 ng/ml). After one week, the expression of thepluripotency marker Oct-4 was analysed using immunostaining. Inhibitionof Activin signalling by SB431542 was found to result in the loss ofOct-4 expression, and the addition of BMP4 was not able to rescue thepluripotent status of EpiSCs. Addition of the natural BMP inhibitorNoggin did not decrease expression of Oct-4. Similar results wereobtained with mouse EpiSCs. Thus, inhibition of Activin/Nodal signallingusing the Activin receptor inhibitor SB431542 induced rapiddifferentiation of EpiSCs, showing that, similarly to hESCs, EpiSCpluripotency depends strictly on Activin/Modal signalling.

Finally, EpiSCs could be derived in CDM supplemented with Activin alone(Table 1), indicating that FGF was not strictly required during thisprocess. However, the presence of FGF improved the overall quality ofthe cultures, suggesting that its function consists in reinforcing theefficiency of Activin signalling, as in hESCs (Vallier, 2005). Takentogether, these observations show that EpiSCs share with mouse ESCs theexpression of standard markers of pluripotency but differ significantlyfrom mouse ESCs in other features which are nevertheless shared withhESCs.

To examine the possibility that EpiSCs are related to germ cells,expression of specific germ cell markers were analysed by immunostainingand RT-PCR. EpiSC were found not to express Blirnpl, which is the firstgene known to be expressed in allocated precursors of primordial germcells (PGCs) just before gastrulation (Vincent, 2005, Ohinata, 2005).Also, EpiSCs were found to lack alkaline phosphase activity, a specificmarker of primordial germ cells (PGCs) in the gastrulating embryo (DeFelici, 1982). Importantly, EpiSCs did not express Stella, which isexpressed in the ICM before implantation, in migrating PGCs atpost-gastrulation stages and in EGs as well as in mouse ES cells (Payer,2003). Moreover, when EpiSCs were derived from embryos carrying a GFPtransgene under the control of the endogenous Stella promoter (Payer,2006), GFP expression was not observed, thereby confirming the absenceof Stella expression. Taken together, these results demonstrate that thepluripotent status of EpiSCs cannot be attributed to a PGC origin.

To further define the origin of EpiSCs, we performed a global analysisof the expression profile of pluripotency markers specific for pre- andpost-implantation embryonic stages in 3 mouse EpiSC lines (passage 25)of the (B6xCBA)FI genetic background and in 2 mouse EpiSC lines (passage15) of the NOD genetic background, using micro-array techniques. Theresulting data were then compared to the expression profile of ICM fromblastocyst embryo, late epiblast from post-implantation embryos, and twomESC lines (RI passage 14 and CGR8 passage 25) using MSD plot analysis(FIG. 2). This comparison showed that mEpiSCs express more common geneswith Epiblast than with ICM or mESCs confirming that mEpiSCs sharesimilarities with their embryonic equivalent. These observation wasconfirmed by RT-PCR analyses showing that EpiSCs did not express GBX2 orRexl, two specific markers of the ICM (Pelton, 2002) that are silencedin early epiblast cells just after implantation but are expressed inmESCs and that transcripts coding for FGF5 (absent in mESCs) and Nodal,two genes specifically expressed in the late epiblast layer (Pelton,2002) after implantation, were clearly detected in EpiSCs. These resultsprovide indication that EpiSCs correspond closely to cells of the lateepiblast layer of the intact post implantation mouse embryo, from whichthey had been derived.

To document further the pluripotent status of EpiSCs, we determinedtheir capacity to differentiate into a wide variety of cell types invitro and in vivo. Differentiation in vitro was achieved by growingEpiSC colonies for 5 days in non-adherent conditions in a mediumsupplemented with 20% Foetal Bovine Serum. The resulting embryoid bodies(EBs) were plated back onto plastic dishes and then grown for anadditional 20 days. We analysed the expression of markers specific forthe derivatives of the three primary germ layers every five days usingRT-PCR. Expression of the pluirpotency marker Oct-4 had disappearedafter 5 days, confirming that EpiSCs lost their pluripotent status inculture conditions favouring differentiation. Generation of mesodermalgerm layer derivatives was confirmed by the expression of Brachyury,MixII (early mesoderm), MyoD, MyF5 (myogenic tissues) and Pecami(vascular tissues). The presence of beating EBs was also observed;confirming the presence of EpiSC derived cardiac cells. Generation ofendoderm germ layer derivatives was confirmed by expression of SoxI7 andFoxA2 which was observed after 5 days of differentiation, as well asexpression of Gata4, Gata6, aFP (liver), PdxI (pancreatic) and Cdx2(gut) marker genes. Finally, expression of specific markers of neuronaldifferentiation (Sox2, Six3, NeuroDI, Islet 1 and p-tubulin III) wasalso detected. Together, these results demonstrate that EpiSCs werecapable of differentiating into derivatives of all three primary germlayers in vitro.

To validate their pluripotency in vivo, EpiSCs colonies were injected inthe testis capsule of immunodeficient mice and the resulting 30teratomas were dissected and sectioned 30 days later. H & E stainingshowed that the teratomas contained a wide variety of tissues, includingmuscle, cartilage, neuronal rosettes, liver and gut thereby reaffirmingthe multi-lineage pluripotency of EpiSCs.

Finally, the capability of EpiSCs to recapitulate normal in vivodevelopment was examined by generating chimaeric embryos usingblastocyst injection. For these experiments, Tau-GFP expressing (B6xCBA)FI EpiSCs were generated by stably transfecting the pTP6 vector usinglipofectamine 2000 (Vallier, 2004). In the first experiment injectedembryos were recovered at 9.5 dpc by dissection, which revealed thepresence of GFP expressing cells (1/17 dissected embryos). This chimaeradisplayed GFP expressing cells in all tissues examined, including liver,limb buds, brain and epidermis. A similar experiment was performed withNOD-EpiSCs and the injected embryos were allowed to develop to term. Twooffspring out 20 embryos EpiSC injected blastocysts showed NODchimaerism at a low level (−10%) by RT-PCR and another by coat colour;germ line transmission was not observed in 56 descendants from the coatcolour chimaera. Together, these results show that EpiSC are capable ofcolonizing a blastocyst and differentiating into a large number oftissues in vivo following normal developmental pathways.

The relative inefficiency of chimaera formation could arise from therequirement to dissociate EpiSC colonies into single cells for theblastocyst injection procedure, thus reflecting their low efficiency ofclonal growth. To address this possibility, mouse embryos at the morulastage were aggregated with EpiSC colonies, and the resulting chimaeraswere transferred at the blastocyst stage to pseudopregnant mice. Nochimaeric offspring were obtained using this approach, thus mirroringsimilar findings by Nagy and co-workers using mouse epiblast cellsdissected from E 5.5 embryos. Taken together, these results provideindication that it is developmental asynchrony between EpiSCs andpreimplantation embryos, rather than developmental potency, which limitstheir capacity to colonise the host embryo.

The hypothesis that Activin and FGF signalling in pluripotency areconserved in mammalian development is supported by the ability ofActivin/Nodal signalling to maintain long-term pluripotency of bothhuman ESCs and mouse EpiSCs. As a further test of this hypothesis, weattempted to derive EpiSCs from rats, a species from which embryonicstem cell derivation has been problematic. Following the method weestablished in the mouse, epiblast layers were dissected from ratembryos at pre-gastrula stages (E 7.5-8.5) and grown onfibronectin-coated or FBS coated plates in CDM supplemented with Activinand FGF. Contrary to the mouse, addition of FGF2 (or FGF4, EGF or HGF)induced differentiation of the early epiblast cultures, providingindication that the role of FGF in pluripotency maintenance is not aswell conserved between mammalian species as that of Activin.Nevertheless, four EpiSC lines were derived out of 14 embryos of theWistar strain and 1 EpiSC line was derived out of 20 embryos from theSprague-Dawley strain using CDM supplemented with Activin alone.

Immunostaining showed that after 10 passages Rat EpiSCs expressed Get-4,Nanog and SSAE-4. Rat EpiSCs appear to share several key properties withmouse EpiSCs and hESCs, including low efficiency of clonal growth andstrict dependence on Activin signalling. Rat EpiSCs were also capable ofdifferentiating in vitro into neuron-like cells, rhythmicallycontracting cells and liver-like cells, suggesting similar potential fordifferentiation as mouse EpiSCs.

Together these results demonstrate that pluripotent stem cells can becultured from widely separated species using chemically defined culturemedium supplemented with Activin. On this basis we conclude that theActivin/Nodal pathway plays a central role in derivation and maintenanceof a novel type of pluripotent stem cells from mammalian embryos,specifically representing the late epiblast cell population just beforegastrulation.

Pluripotent embryonic stem cells had previously been obtained byculturing blastocysts or isolated ICMs of mouse and primate embryos. Thedata set out herein shows that pluripotent stem cell lines can also begenerated from the late epiblast layer isolated after implantation (justbefore gastrulation), using Activin and FGF (mouse EpiSCs) in chemicallydefined culture conditions. Such EpiSCs can be grown extensively invitro while maintaining their capacity to differentiate both in vitroand in vivo into a large variety of tissues, thereby demonstrating theirpluripotent status.

EpiSCs differ from mouse ESCs not only in their embryonic origin butalso by the signalling pathway maintaining their pluripotent status(Activin vs LIF), their expression profile, their low efficiency tocolonise a blastocyst, and their low efficiency of clonal growth asisolated single cells. Importantly, EpiSCs express specific markers ofthe epiblast layer of the post-implantation embryo, including FGF5, andthey lack the expression of specific markers of the ICM, including Rexl.In this regard they resemble the early primitive ectoderm-like (EPL)cells that were established by growing mouse ES cells in a 10 mediumconditioned by the hepatic cell line HePG2 in the absence of LIF(Rathjen, 1999). However, EPL cells show some in vitro restriction fromdifferentiation into neuroectoderm; in addition, LIF can revert EPLcells to ES cells. Neither of these two features is shared by EpiSCs.The lack of AP activity in EpiSCs and the absence of Blirnpl expressionalso exclude the possibility of EpiSCs being related to PGCs.Consequently, EpiSCs represent a novel type of pluripotent embryonicstem cells sharing several characteristics with late epiblast cells invivo.

The dependence of EpiSC pluripotency on Activin/Nodal signalling notonly distinguishes them from mouse ESCs, but also highlights theirresemblance to late epiblasts. Our results show that pluripotent stemcells of the late epiblast require only Activin/Nodal signalling tomaintain their pluripotent status. The function of Activin/Nodalsignalling in pluripotency is substantially conserved throughoutmammalian evolution since hESCs and rat EpiSCs are also maintained bythe Activin signalling pathway, thereby providing indication that EpiSCscould be derived from other species using this approach.

Besides their value for understanding basic mechanisms controlling earlydevelopment, EpiESCs also offer a promising resource for transgenicalteration of the mammalian germline. Indeed, our success in derivingNOD mouse and rat EpiESCs provide indication that the protocol describedhere could be used to derive pluripotent cells in a wider range ofmammalian species. Accordingly, EpiSCs could greatly facilitate thegeneration of transgenic livestock species, although the efficiency ofEpiSCs in colonizing blastocysts was low. Nuclear transfer couldrepresent an advantageous approach. Indeed, ESCs represent the bestdonor cells for nuclear reprogramming in the mouse (Meissner 2006) andthe application of this approach to other species is largely limited bythe absence of equivalent pluripotent cells. EpiSCs could represent aviable alternative for such purposes.

TABLE 1 No. Epiblasts Lines derived Rat Rat Mouse Sprague- MouseSprague- Rate B6 NOD Wistar Dawley d.p.c. Temp Matrix Growth factors B6NOD Wistar Dawley % 9 6.5 37° C. fibro Activin + FGF₂ 9 100 6 5.5 37° C.fibro Acticin + FGF₂ 5 83 5 6.5 37° C. fibro Activin + FGF₂ + 4 80Noggin ~14 8.5 38° C. FCS Activin 4 35 −20 8.5 37° C. fibro Activin 1 5

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The invention claimed is:
 1. A method of producing a population ofisolated mouse or rat pluripotent Epiblast Stem Cells (EpiSCs) that aresubstantially free from other cell types, the method comprising thesteps of: a) obtaining a rat or mouse post-implantation embryo; b)isolating the late epiblast layer of the post-implantation embryo andmicrodissecting it away from extraembryonic tissues; c) culturing themicrodissected late epiblast layer of step (b) under conditions in whichthe Activin/Nodal signaling pathway is activated such that a populationof isolated mouse or rat pluripotent EpiSCs that are substantially freefrom other cell types is produced.
 2. The method of claim 1 wherein theActivin/Nodal pathway is activated by an Activin/Nodal pathway activatorselected from the group consisting of activin A, activin B, activin AB,TGFbeta1, GDF-3 and Nodal.
 3. The method of claim 1 wherein thepopulation of isolated mouse or rat pluripotent EpiSCs that aresubstantially free from other cell types is unresponsive to LIF.
 4. Themethod of claim 1 wherein the population of isolated mouse or ratpluripotent EpiSCs that are substantially free from other cell typesexpress Oct4, Nanog, Sox2, Fgf5 and Nodal and do not express Blimp1,Stella, alkaline phosphatase, Gbx2 or Rex1.
 5. The method of claim 1wherein the mouse or rat pluripotent EpiSCs retain their pluripotencywhen continuously cultured under conditions in which the Activin/Nodalsignaling pathway is activated.
 6. The method of claim 1 or 5 whichoptionally comprises supplementing the culture with FGF2.